5.01 "Search And Rescue Part 2"
- Carter launches a rescue operation for several victims of an off-world massive explosion and must combat Michael and his army who also wish to recover the survivors.
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5.02 "The Seed"
- Dr. Carson Beckett is removed from stasis because he's the only one who can take action to figure a way out of a serious dilemma before it’s too late for some of his close friends.
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5.03 "Broken Ties"
- Ronon is captured by a Wraith in an attempt to turn him into a worshipper, but it is the Satedan Tyre who may have the most significant influence on Ronon’s destiny.
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5.04 "The Daedalus Variations"
- Sheppard's team boards an abandoned Daedalus in orbit over Atlantis and gets stuck jumping from one alternate reality into another until they arrive in one reality that could be their last when the ship is boarded by an alien species.
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5.05 "Ghost In The Machine"
- Surviving human form Replicators wish to achieve ascension by uploading their consciousnesses into subspace to live indefinitely as fields of energy, but Atlantis is put into danger when their experiment yields some surprising results.
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5.06 "The Shrine"
- McKay ends up suffering from the Pegasus verion of Alzheimer's that is called 'Second Childhood', and he very quickly loses his memories and becomes quite childlike. His condition is diagnosed too late to operate, but Ronon may have the answer that will save him ... if it isn't too late.
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5.07 "Whispers"
- Sheppard and Beckett join Maj. Anne Teldy’s team on a planet with one of Michael’s research facilities for the early versions of his human-iratus hybrids concealed inside a cave system. Unfortunately, the explorers have a role in setting loose creatures that hunt down each of them as they get separated in a blinding fog.
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5.08 "The Queen"
- Teyla poses as Todd’s Queen to represent his hive in negotiations with an allied hive, but tension escalates as the alliance’s territories are threatened by another Wraith hive.
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5.09 "Tracker"
- Keller is abducted by the Runner Kiryk who brought the Wraith to a village on a planet where she, McKay, and Ronon were visiting. After helping the villagers to safety, McKay and Ronon set out to rescue Keller, running into booby traps left by the Runner along the way.
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5.10 "First Contact Part 1"
- Dr. Daniel Jackson comes to do research into the history of the Atlantian Ancient Janus who built a timeship in a puddle jumper 10,000 years ago. During his visit, a new enemy in the galaxy gets revealed.
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5.11 "The Lost Tribe Part 2"
- McKay and Daniel are caught in the middle of the war between the Wraith and another powerful race in the Pegasus Galaxy. Sheppard teams up with the Travelers to rescue the two after the Apollo falls into enemy hands.
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4.12 Working title: "Outsiders"
- Written by: Alan McCullough
- Directed by:
- Storyline:
- Production:
- "We have an idea for episode 12 (and are looking for a suitable location)..." — Joseph Mallozzi in his personal blog, March 22, 2008.
- "Alan is focused on his third script..." — Joseph Mallozzi in his personal blog, April 11, 2008.
- "Finally, in response to those complaining about an uneven balance in the types of stories being told this year - like last year, everyone will be getting an episode. The reason I haven’t discussed the Sheppard story is because, unlike Ronon, McKay, and Teyla, his story falls in the back half of the season. Ronon has Broken Ties. Teyla has The Queen. McKay has The Shrine. And Sheppard will have CSI: Atlantis (and possibly Hexed if we can make it work)." — Joseph Mallozzi in his personal blog, April 17, 2008.
- "Next to thinking up with episode titles, coming up with names for aliens and off-world villagers is one of the most challenging aspects of this job. In preparation for an upcoming script, we recently set aside time to brainstorm some terrific names. So far, we’ve got: Philip Seymour Hoffan, Felicity Hoffan, Carey the story’s pariah (aka Pariah Carey), and, my favorite, David Hassel the Hoffan (aka David Hassel Hoffan). An entire afternoon well spent." — Joseph Mallozzi in his personal blog, April 28, 2008.
- "We have Alan McCullough’s location episode (q.v. yesterday‘s David Hassel Hoffan entry)..." — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Outsiders will be Alan’s follow-up to The Queen..." — Joseph Mallozzi in his personal blog, May 8, 2008.
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5.xx "Inquisition"
- Written by: Alex Levine
- Directed by:
- Storyline:
- Production:
- "Alex has been hard at work on his very first Atlantis script, Inquisition, that will address an issue a number of you have brought up of late." — Joseph Mallozzi in his personal blog, March 20, 2008.
- "I’ve mentioned episodes 1-11 in recent blog entries and even mentioned the back half eppy, Inquisition, that Alex Levine is writing." — Joseph Mallozzi in his personal blog, March 22, 2008.
- AMZ writes: "I have a question about Inquisition. Will there be clips from previous episodes in it?" Answer: "Looks like it." — Joseph Mallozzi in his personal blog, March 23, 2008.
- "Alex Levine’s Inquisition (in which Atlantis is finally made to answer for past transgressions)..." — Joseph Mallozzi in his personal blog, April 29, 2008.
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5.xx Working title: "Prodigal"
- Written by: Carl Binder
- Directed by:
- Storyline:
- Production:
- "Carl is spinning ideas for his third [script]..." — Joseph Mallozzi in his personal blog, April 11, 2008.
- "We spent the afternoon spinning Carl’s idea, a story Alan is calling “The Red Shirt Diaries”." — Joseph Mallozzi in his personal blog, April 15, 2008.
- "Carl Binder’s latest (the beat sheet arrived on my desk late this afternoon and I’m going to try to read it tomorrow morning)..." — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Well, I finally did make it back to the production offices in time to [...] give Carl notes on his beat sheet (formerly The Red Shirt Diaries then First Day and now ???)." — Joseph Mallozzi in his personal blog, May 1, 2008.
- "Carl’s script, formerly titled The Red Shirt Diaries before being re-titled to First Day, has become Prodigal." — Joseph Mallozzi in his personal blog, May 8, 2008.
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5.15 Martin Gero's Written and Directed By Spectacular
- Written by: Martin Gero
- Directed by: Martin Gero
- Storyline:
- Production:
- "Martin Gero 'written and directed by spectacular'..." — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Martin almost had himself a new story today. I say almost because, after spinning out what he felt was a wonderfully exciting idea, Martin returned to his office and, in the process of writing it up, came to the conclusion that, hey, this concept has the potential to go wrong in so many different ways. So, he’s back at Square #1. ... Well, hey. Marty G. just dropped by to pitch out his new, wonderfully exciting idea for Episode #15. We all love it. I suggested he rush back to his office and write it up before he changes his mind. Again." — Joseph Mallozzi in his personal blog, May 8, 2008.
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5.16 Working title: "Remnants"
- Written by: Joseph Mallozzi
- Directed by:
- Storyline:
- Production:
- "Looking way ahead, I’ve talked myself into the #16 spot with “a very special Stargate Atlantis” (apologies to James Stewart), while we’ve got some other potential stories floating about in search of definitive slot." — Joseph Mallozzi in his personal blog, March 4, 2008.
- "...my “a very special Stargate Atlantis” which quite possibly may see the return of the lovely Kari Wuhrer [Sheppard's ex-wife Nancy]..." — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Yes, it feels like not that long ago I was prepping episode #3 and now, here I sit, thinking about thinking about episode #16. Yes, I’ll eventually start making headway but, at this point in a story‘s development, it‘s so easy to get distracted by seemingly more pressing matters..." — Joseph Mallozzi in his personal blog, May 7, 2008.
- "Skip over that big, blank space at the #15 slot and you come to my final episode of the season, tentatively titled Remnants. A little more progress today which took the form of my promising to have a beat sheet ready for Monday. I guess there’s nothing left to do now but write the damn thing." — Joseph Mallozzi in his personal blog, May 8, 2008.
- This episode is scheduled for start of filming in late July according to Joseph Mallozzi in his personal blog, May 8, 2008.
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5.19 Working title: "CSI: Atlantis"
- Written by: Robert C. Cooper
- Directedy by: Robert C. Cooper
- Storyline:
- Production:
- "...and episodes 19 (which Rob Cooper will be writing/directing/producing)..." — Joseph Mallozzi in his personal blog, March 22, 2008.
- "Finally, in response to those complaining about an uneven balance in the types of stories being told this year - like last year, everyone will be getting an episode. The reason I haven’t discussed the Sheppard story is because, unlike Ronon, McKay, and Teyla, his story falls in the back half of the season. Ronon has Broken Ties. Teyla has The Queen. McKay has The Shrine. And Sheppard will have CSI: Atlantis (and possibly Hexed if we can make it work)." — Joseph Mallozzi in his personal blog, April 17, 2008.
- "CSI: Atlantis which will be helmed by Robert C. Cooper..." — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Robert Cooper actually came in and he pitched an idea for episodes 19 and 20, which we thought was great, so we know what we’re working towards." — Joseph Mallozzi in MGM interview, April 29, 2008.
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5.20 Finale
- Story by: Robert C. Coopoer
- Teleplay by: Paul Mullie
- Directed by:
- Storyline:
- Production:
- "It really hit home this afternoon when I glanced up at the whiteboard and saw the big, empty space beneath the Season 5 heading and beside the numbers 1 through 20. Marty G. helpfully filled in areas with the following titles: Premiere, Mid-Season Two Parter, and Finale. Awesome! 4 down and 16 to go!" — Joseph Mallozzi in his personal blog, October 24, 2007.
- This episode will be the show's 100th. When asked if it will be like the 100th episode of Stargate SG-1 "Wormhole X-Treme", which was not too serious, Joseph Mallozzi replied, "Since it will be the season-ender, it will not be comical." — Joseph Mallozzi in his personal blog, October 27, 2007.
- PG15 writes: "Who’s getting the great honor of writing the 100th episode of Stargate Atlantis, 520?" Answer: "Right now, it looks like Paul will be doing the honors." — Joseph Mallozzi in his personal blog, March 23, 2008.
- "To those asking - no, the 100th episode will not be a comedy. We have something big in mind and are already in the planning stages. Speaking of episodes…" — Joseph Mallozzi in his personal blog, April 29, 2008.
- "Robert Cooper actually came in and he pitched an idea for episodes 19 and 20, which we thought was great, so we know what we’re working towards." — Joseph Mallozzi in MGM interview, April 29, 2008.
- "...and that season finale I was talking about. Which leaves one mystery slot." — Joseph Mallozzi in his personal blog, April 29, 2008.
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5.xx Untitled Extreme Shep-Whumpage Story (Hexed or something else)
- Story by: Robert C. Cooper and Alan McCullough
- Teleplay by: Alan McCullough
- Directed by:
- Storyline:
- Production:
- "A final of Alan McCullough’s Daedalus Variations came out today and we shifted focus to Alan’s second - extreme Shep-whumpage - script, co-storied by Robert C. Cooper." — Joseph Mallozzi in his personal blog, February 11, 2008.
- "Alan is mulling over a possible story to slip into the #9 slot as the script originally envisioned for that spot ran into a “creative snafu” that a) moved it into the back half and b) may necessitate a change in perspective." — Joseph Mallozzi in his personal blog, January 20, 2008.
- "Yes, the extreme Shep-whump episode has been moved to the back half, leaving a big yawning empty space in the #9 slot." — Joseph Mallozzi in his personal blog, February 22, 2008.
- "That’s a script in search of a home - and a possible transplant. We’ll see how things develop." — Joseph Mallozzi in his personal blog, February 5, 2008.
- "There’s also that episode idea that was originally slotted for the first half that is now free-floating but should find a home in one of the remaining four slots." — Joseph Mallozzi in his personal blog, March 22, 2008.
- "Alan is focused on his third script..." — Joseph Mallozzi in his personal blog, April 11, 2008.
- Chevron 7 writes: “Alan’s “extreme Shep whump” episode - if it’s not too much of a spoiler is it more physical, mental or both?” Answer: "If we move ahead with the idea, it will be both." — Joseph Mallozzi in his personal blog, April 16, 2008.
- "Finally, in response to those complaining about an uneven balance in the types of stories being told this year - like last year, everyone will be getting an episode. The reason I haven’t discussed the Sheppard story is because, unlike Ronon, McKay, and Teyla, his story falls in the back half of the season. Ronon has Broken Ties. Teyla has The Queen. McKay has The Shrine. And Sheppard will have CSI: Atlantis (and possibly Hexed if we can make it work)." — Joseph Mallozzi in his personal blog, April 17, 2008.
- "Hexed is still a possibility." — Joseph Mallozzi in his personal blog, April 30, 2008.
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5.xx Possible Revisit to SG-1's Shelved "Yesterday, Today, and Tomorrow"
- Story by: Joseph Mallozzi
- Written by:
- Directed by:
- Storyline:
- Production:
- "... 1) an impromptu gathering of the writers to spin four possible new story ideas including a sequel to that season 4 episode and the possibility of revisiting the SG-1-themed and shelved Yesterday, Today, and Tomorrow..." — Joseph Mallozzi in his personal blog, February 14, 2008.
- "Yesterday, Today, and Tomorrow" is a time travel x2 story originally pitched by Mallozzi for SG-1's Season Ten, but was replaced by Alan McCullough's "The Road Not Taken". Alex Levine wrote of the shelving of Mallozzi's idea in his scifi.com blog: "When writers are coming up with new ideas, it’s often the case that one story, or part of a story, is too similar to a story idea that has already been written or agreed upon (or purchased, as is the case with freelance writers). When this happens, we say the idea “steps on” the other. And that happens quite a lot. So often really good ideas get squashed because they would be repetitive. And it happened on SG-1 just recently with two stories that at first glance don’t appear to be too similar but once you take a good look at them they are. Joe Mallozzi had come up with a time travel story, and Alan McCullough was working on an alternate reality story. Now it doesn’t take a genius to realize that if you go back in time, and change the future, that you’d be dealing with a present tense alternate reality. So they stepped on each other. And only one went ahead. But you’ll have to wait until later in the season until I tell you which one went ahead… but I’m taking the political middle ground – in my opinion, both episodes would be a lot of fun." — Alex Levine, Script Coordinator, SciFi.com Blog, July 25, 2006.
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